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Divergent Transcription: A Driving Force for New Gene Origination?
Xuebing Wu,Phillip A. Sharp +1 more
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TLDR
The authors proposed that divergent transcription from promoters and enhancers may shape the evolution of the genome by new gene origination, and showed that the divergence from active gene transcription can shape the evolutionary process of the mammalian genome.Abstract:
The mammalian genome is extensively transcribed, a large fraction of which is divergent transcription from promoters and enhancers that is tightly coupled with active gene transcription. Here, we propose that divergent transcription may shape the evolution of the genome by new gene origination.read more
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Journal ArticleDOI
Landscape of transcription in human cells
Sarah Djebali,Carrie A. Davis,Angelika Merkel,Alexander Dobin,Timo Lassmann,Ali Mortazavi,Ali Mortazavi,Andrea Tanzer,Julien Lagarde,Wei Lin,Felix Schlesinger,Chenghai Xue,Georgi K. Marinov,Jainab Khatun,Brian A. Williams,Chris Zaleski,Joel Rozowsky,Marion S. Röder,Felix Kokocinski,Rehab F. Abdelhamid,Tyler Alioto,Igor Antoshechkin,Michael T. Baer,Nadav Bar,Philippe Batut,Kimberly Bell,Ian Bell,Sudipto K. Chakrabortty,Xian Chen,Jacqueline Chrast,Joao Curado,Thomas Derrien,Jorg Drenkow,Erica Dumais,Jacqueline Dumais,Radha Duttagupta,Emilie Falconnet,Meagan Fastuca,Kata Fejes-Toth,Pedro G. Ferreira,Sylvain Foissac,Melissa J. Fullwood,Hui Gao,David Gonzalez,Assaf Gordon,Harsha P. Gunawardena,Cédric Howald,Sonali Jha,Rory Johnson,Philipp Kapranov,Brandon King,Colin Kingswood,Oscar Junhong Luo,Eddie Park,Kimberly Persaud,Jonathan B. Preall,Paolo Ribeca,Brian A. Risk,Daniel Robyr,Michael Sammeth,Lorian Schaffer,Lei-Hoon See,Atif Shahab,Jørgen Skancke,Ana Maria Suzuki,Hazuki Takahashi,Hagen Tilgner,Diane Trout,Nathalie Walters,Huaien Wang,John A. Wrobel,Yanbao Yu,Xiaoan Ruan,Yoshihide Hayashizaki,Jennifer Harrow,Mark Gerstein,Tim Hubbard,Alexandre Reymond,Stylianos E. Antonarakis,Gregory J. Hannon,Morgan C. Giddings,Morgan C. Giddings,Yijun Ruan,Barbara J. Wold,Piero Carninci,Roderic Guigó,Thomas R. Gingeras,Thomas R. Gingeras +87 more
TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
Journal ArticleDOI
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Guoliang Li,Xiaoan Ruan,Raymond K. Auerbach,Kuljeet Singh Sandhu,Meizhen Zheng,Ping Wang,Huay Mei Poh,Yufen Goh,Joanne Lim,Jingyao Zhang,Hui Shan Sim,Su Qin Peh,Fabianus Hendriyan Mulawadi,Chin Thing Ong,Yuriy L. Orlov,Shuzhen Hong,Zhizhuo Zhang,Steve Landt,Debasish Raha,Ghia Euskirchen,Chia-Lin Wei,Weihong Ge,Huaien Wang,Carrie A. Davis,Katherine I. Fisher-Aylor,Ali Mortazavi,Mark Gerstein,Thomas R. Gingeras,Barbara J. Wold,Yi Sun,Melissa J. Fullwood,Edwin Cheung,Edwin Cheung,Edison T. Liu,Wing-Kin Sung,Wing-Kin Sung,Michael Snyder,Yijun Ruan,Yijun Ruan +38 more
TL;DR: In conclusion, this study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells through widespread promoter-centered intragenic, extragenics, and intergenic interactions.
Journal ArticleDOI
Epigenetic Regulation by Long Noncoding RNAs
TL;DR: A glimpse into the molecular biology of multiple emerging lncRNA systems reveals the “Wild West” landscape of their functions and mechanisms and the key problems to solve in the years ahead toward understanding these intriguing macromolecules.
Journal ArticleDOI
Bidirectional gene organization: a common architectural feature of the human genome.
TL;DR: It is shown that some small percentage of the genes counted or not counted as close to one another will change status as more information about each locus is gathered, as refinement of the human genome continues.
Journal ArticleDOI
Gene Loops Enhance Transcriptional Directionality
Sue Mei Tan-Wong,Judith B. Zaugg,Jurgi Camblong,Zhenyu Xu,David W. Zhang,Hannah E. Mischo,Aseem Z. Ansari,Nicholas M. Luscombe,Nicholas M. Luscombe,Nicholas M. Luscombe,Lars M. Steinmetz,Nick J. Proudfoot +11 more
TL;DR: It is demonstrated that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent transcription of ncRNAs.
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